Incipiens: A New Beginning
by Legionary Prime
Summary: The treachery of the Prophets was discovered early on, changing the course of the Human-Covenant War. The UNSC are en route to the planet Harvest to make a treaty with the Covenant Reformists, but an ancient discovery will shake the galaxy to its core. T for some violence and some swearing. Rewrite.


**A/N I am sorry for the past times I messed up with Incipiens. But, I've improved a lot this past month. Looking for new writing tips to help improve and I've think I' got some improvement here. This is my latest version of my Halo/Mass Effect crossover. It is a different take then what I had originally planed. The NCSA and the Capital are no longer included. It would made the Halo species WAY over powered than they already were. I am also going to be making the Citadel species stronger. The Quarian fleet is doubled in size, there was no ship restriction on the Citadel races and the Turians have a fleet half the size of the new Quarian fleet. I am also fixing the Catalyst problem or 'Catalyst Effect' as I like to call it. I am not revealing anything I have planned for it but it is going to satisfy fans who were disappointed by ME3's ending. I am still working through the final thinking process of the Catalyst so have no fear.**

**I know this chapter is short but next one is going to be longer.**

**NOTE: Going to change the fact about the Turian's fleet. I am not going to make it like I said, but I am increasing its strength some more.**

**Disclaimer: I don't own Halo or Mass Effect. I just own this story and any OC's or other things that weren't part of their respective universes.**

At the start of the Human-Covenant war, a dark secret was discovered. The Prophets of Truth, Mercy, and Regret conspired to take control of the Covenant. But, one Sangheili warrior discovered the truth. Thel'Vadam was sent by the leader of the Sangheili to inspect the Forerunner Dreadnought at High Charity in secret. Such an act would be considered treason. What he found shook him to the core. A message broadcasted all over High Charity.

"Those who follow the false Prophets would only lead them to their doom. You call this Reclamation...this is Reclaimer. They are the Forerunners true children, the inheritor of all they left behind. You have been lied to. I am Mendicant Bias and this is my last testament to atone for my sins."

This started the Great Schism, many years than it should have started. A group of San' Shyuum ordered the removal of the current High Prophets. The legislation was passed, but when they arrived to arrest them, they fled. The Jiralhanae Chieftain Tartarus and current Arbiter Ripa' Moramee fled as well with their forces to join the traitorous Prophets

New High Prophets, Vigilance, Distinction, and Malice. reformed the new Covenant, calling themselves the Covenant Reformists while the ones who follow the traitors are called the Loyalists for going by the old ways.

The Reformists contacted the UNSC and explained what happened to them. Skeptical, they agreed to meet at the former UNSC colony, Harvest, in the Epsilon Indi System.

But, things did not go as planned.

_February 4th, 2531_

_"Captain's log: February 4th, 2531. Five years... Five long years, that's how long it took us to get Harvest. back. At first it was going well. Then...setback after setback. Loss after loss. What was going to be a quick and decisive win, became five years of hell. But, that changed with the Great Schism. Word spread of the Civil War among the Covenant and many, including myself, was shocked to see a sect of the Covenant wanting to help us. Then started the Cold War, between the UNSC and the Covenant Reformists against the Loyalists. The Reformists sent a nonaggression treaty to the UNSC, asking for an alliance. The Reformists will pull out of any occupied UNSC system and help rebuild what was lost. To set an example, they gave back Harvest. The place where it all began. Me and the UNSC Spirit of Fire were sent to make sure everything was going according to plan. To make sure the treaty gets signed. An important asset from the Office of Naval Intelligence will be coming aboard to sign the treaty. I don't trust this guy._

_Cutter, out."_

Captain James Cutter was watching from the view screen, the image of Harvest. It has seen better days, but with the recent treaty, it can return to its former glory once more. The view screen change to the image of a soldier with low-cut hair and dark eyes. He wore the standard UNSC marine armor.

"Sergeant Forge, status?" asked Cutter.

_"All clear along this sector, Captain. I am picking up some strange readings so I am going to check it out. Afterwards, I'll go to the rendezvous point and meet with Doctor. Church and Ambassador Harper," said Forge._

"Keep up the good work Sergeant," said Cutter when a woman with brown, tied up hair and dark eyes and wore a lab coat appeared behind him.

"Serina, any changes to the area, like Forge said?" asked Cutter.

A hologram of a black haired woman with a white dress appeared.

"_I am detecting an unusual energy reading coming near the vicinity of Sergeant Forge's location. It appears to be a large structure of some kind," _said the Artificial Intelligence known as Serina.

"I haven't picked up anything yet. Something must be blocking my scanners. Wait, I see something up ahead. Its the 'True' Covenant. Shepard, pull the Warthog to behind that rock face so they don't see us," said Forge.

Cutter wasn't expecting the 'True' Covenant to be on Harvest.

"I am going down there soon. I need to examine those artifacts to see fi they belong to those 'Forerunners' the Covenant mentioned," said the woman.

_"Sorry Professor Anders, but that is a no go. Until I find out the situation here, you're not coming down,"_said Forge while Anders ignored him.

_With Forge_

After Shepard pulled the Warthog from eye distance, he decided to scout on ahead once he saw the Covenant gone. Forge crawled on the snow until he reached the cliff edge. He pulled out some binoculars. "Let's have one last look see."

He saw two Sangheili, dubbed Dishonored Sangheili by their own people. One wore the gold armor of a Zealot and the other was the Arbiter. The Sangheili have their own Arbiter after the this one's defection. He is true to the old ways by heart.

_"The Hierarchs grow impatient, we can't delay no longer." said the Arbiter._

_"What if the infection and the heretics defile the relic?" the Zealot dared to say to the Arbiter._

_The Arbiter clenched his fist "I care not for your little life open the relic," the Arbiter commanded._

_The Zealot complied and went on ahead to order the Unggoy to open the doors to the mysterious relic. Two Sangheili, wearing red armor came to the Arbiter next._

_"Arbiter, we've captured the heretics. They were attempting to make an alliance with the Human filth. They are in the holding cells." said the red Sangheili._

The Arbiter laughed. The alien structure started to open as Unggoy walked into it.

"Well, well. Open sesame," said Forge as he put back his binoculars.

The Arbiter thought he heard something and turned to see no one at the place where Forge used to be.

* * *

_"I am experiencing such a mixture of anticipation and dread. All preparations are complete for my installation. In accordance with the final dictum of the Ecumene Council, I have released myself of all remaining connections to my former station. This was not difficult. What was could never be again. We had seen to that quite thoroughly. Prior to my final journey through the great portal, a gathering of my fellow monitors was convened upon the Lifeworkers' crèche to distribute the final Index collection. It was most unusual to have this vessel of rebirth play host to such an event, even though Lifeworker ships were the only ones still allowed slipspace permissions. Lifeworkers were responsible for getting us to our places on the active facilities of the Array. While all of this was in accordance with the plan, one entirely unsatisfactory breakdown remained. We had no contact with the Domain._

_The history of all Forerunners was now lost to us. We relied upon the permanence of the Domain to preserve our record of the events that led to this point. But without that record, would future civilizations know anything about us? Or only of our weapons? My fellow Monitor, 049 Abject Testament, had only one comment on this before we went our separate ways."_

_"We deserve to be forgotten."_

_"Perhaps...perhaps. But now, the portal opens - and through it, the familiar shape awaits._

_Halo... Home."_

**A/N This is it, my new Incipiens. The dialog from the Halo Wars bit is changed as they are at Harvest for a different reason than finding the relic. The relic will play a bigger role next chapter. Anyways, be sure to check out the fic Mass Effect New Origins V2, its what inspired me to write a Halo/ME crossover. There will be some changes to the Halo story that will eventually come together in the end in case you are worried. Like, how will Halo play out or the Battle of Earth and the Ark in Halo 3? Also, the Mass Effect events will come together as well. The next chapter will feature the POV from the ME races.**

**Next chapter will be up by the end of the week and look for this story on Deviantart in the next week or so.**


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